Detecting hybridization in Chilean species of the genus Baccharis L

The genus Baccharis in Chile is an extraordinary example of admixture, previously described only morphologically and chemically. In Chile, the genus forms a homoploid complex with at least 16 species and 21 hybrids. Genotyping-by-Sequencing (GBS) was used to clarify the hybrid character of Baccharis × intermedia, which originated from the species B. macraei and B. linearis. Additionally, B. vernalis, another species with a morphological resemblance to B. macraei, was subjected to analysis to ascertain its role in the hybridization process. A total of 11,006 SNPs and 72 individuals were analysed using Treemix, D- and f-statistics, which revealed genetic evidence of hybridization between B. macraei and B. linearis. Furthermore, other genetic indicators, such as a high level of heterozygosity, also provided evidence of the hybrid nature of Baccharis × intermedia. Additionally, one individual exhibited strong genetic proportions derived from B. vernalis, B. macraei, and B. linearis. Distinct individuals were clustered using sparse Non-Negative Matrix Factorization (sNMF) into five distinct groups, representing the described species and the hybrid. B. macraei exhibited division into a northern and a southern subpopulation. The morphological and chemical evidence of the hybrid character of Baccharis × intermedia is corroborated by genetic data. Further, the most likely evolutionary scenario is a hybrid swarm. Genetic differentiation between B. linearis and B. macraei indicates separation prior to secondary contact. The close relationship of B. macraei and B. vernalis was confirmed, suggesting that it may emerge as a vicariant species on different soil types.